You will be assigned a particular berth with your ticket, and they'll check tickets when boarding the train at the other stops, so you won't have to worry about someone pinching it. You should be able to ask Baolau to give you an upper berth; despite the snazzy website it's still a manual process on their end (although they do seem to be fine).

Haven't done normal soft sleeper to Sapa, but have on the refurbished trains south of Hanoi. It was fine, which is to say, the Seat61 description was accurate. Not quite as comfy as a French couchette train 5 years ago. To be honest, the private carriages aren't exactly the height of luxury anyway (perhaps about as comfy as a 4-berth French couchette), so you shouldn't worry about missing out on much!